Microevolution of extensively drug-resistant tuberculosis in Russia.

Extensively drug-resistant (XDR) tuberculosis (TB), which is resistant to both first- and second-line antibiotics, is an escalating problem, particularly in the Russian Federation. Molecular fingerprinting of 2348 Mycobacterium tuberculosis isolates collected in Samara Oblast, Russia, revealed that 72%belonged to the Beijing lineage, a genotype associated with enhanced acquisition of drug resistance and increased virulence. Whole-genome sequencing of 34 Samaran isolates, plus 25 isolates representing global M. tuberculosis complex diversity, revealed that Beijing isolates originating in Eastern Europe formed a monophyletic group. Homoplasic polymorphisms within this clade were almost invariably associated with antibiotic resistance, indicating that the evolution of this population is primarily driven by drug therapy. Resistance genotypes showed a strong correlation with drug susceptibility phenotypes. A novel homoplasic mutation in rpoC, found only in isolates carrying a common rpoB rifampicin-resistance mutation, may play a role in fitness compensation. Most multidrug-resistant (MDR) isolates also had mutations in the promoter of a virulence gene, eis, which increase its expression and confer kanamycin resistance. Kanamycin therapy may thus select for mutants with increased virulence, helping preserve bacterial fitness and promoting transmission of drug-resistant TB strains. The East European clade was dominated by two MDR clusters, each disseminated across Samara. Polymorphisms conferring fluoroquinolone resistance were independently acquired multiple times within each cluster, indicating that XDR TB is currently not widely transmitted. © 2012 by Cold Spring Harbor Laboratory Press

On an exponential attractor for a class of PDEs with degenerate diffusion and chemotaxis

In this article we deal with a class of strongly coupled parabolic systems that encompasses two different effects: degenerate diffusion and chemotaxis. Such classes of equations arise in the mesoscale level modeling of biomass spreading mechanisms via chemotaxis. We show the existence of an exponential attractor and, hence, of a finite-dimensional global attractor under certain 'balance conditions' on the order of the degeneracy and the growth of the chemotactic function

Critical dynamics of self-gravitating Langevin particles and bacterial populations

We study the critical dynamics of the generalized Smoluchowski-Poisson system (for self-gravitating Langevin particles) or generalized Keller-Segel model (for the chemotaxis of bacterial populations). These models [Chavanis & Sire, PRE, 69, 016116 (2004)] are based on generalized stochastic processes leading to the Tsallis statistics. The equilibrium states correspond to polytropic configurations with index $n$ similar to polytropic stars in astrophysics. At the critical index $n_{3}=d/(d-2)$ (where $d\ge 2$ is the dimension of space), there exists a critical temperature $\Theta_{c}$ (for a given mass) or a critical mass $M_{c}$ (for a given temperature). For $\Theta>\Theta_{c}$ or $M<M_{c}$ the system tends to an incomplete polytrope confined by the box (in a bounded domain) or evaporates (in an unbounded domain). For $\Theta<\Theta_{c}$ or $M>M_{c}$ the system collapses and forms, in a finite time, a Dirac peak containing a finite fraction $M_c$ of the total mass surrounded by a halo. This study extends the critical dynamics of the ordinary Smoluchowski-Poisson system and Keller-Segel model in $d=2$ corresponding to isothermal configurations with $n_{3}\to +\infty$. We also stress the analogy between the limiting mass of white dwarf stars (Chandrasekhar's limit) and the critical mass of bacterial populations in the generalized Keller-Segel model of chemotaxis

The Presampler for the Forward and Rear Calorimeter in the ZEUS Detector

The ZEUS detector at HERA has been supplemented with a presampler detector in front of the forward and rear calorimeters. It consists of a segmented scintillator array read out with wavelength-shifting fibers. We discuss its desi gn, construction and performance. Test beam data obtained with a prototype presampler and the ZEUS prototype calorimeter demonstrate the main function of this detector, i.e. the correction for the energy lost by an electron interacting in inactive material in front of the calorimeter.Comment: 20 pages including 16 figure

Finite mass self-similar blowing-up solutions of a chemotaxis system with non-linear diffusion

For a specific choice of the diffusion, the parabolic-elliptic Patlak-Keller-Segel system with non-linear diffusion (also referred to as the quasi-linear Smoluchowski-Poisson equation) exhibits an interesting threshold phenomenon: there is a critical mass $M_c>0$ such that all the solutions with initial data of mass smaller or equal to $M_c$ exist globally while the solution blows up in finite time for a large class of initial data with mass greater than $M_c$. Unlike in space dimension 2, finite mass self-similar blowing-up solutions are shown to exist in space dimension $d?3$

Local and Global Well-Posedness for Aggregation Equations and Patlak-Keller-Segel Models with Degenerate Diffusion

Recently, there has been a wide interest in the study of aggregation equations and Patlak-Keller-Segel (PKS) models for chemotaxis with degenerate diffusion. The focus of this paper is the unification and generalization of the well-posedness theory of these models. We prove local well-posedness on bounded domains for dimensions $d\geq 2$ and in all of space for $d\geq 3$, the uniqueness being a result previously not known for PKS with degenerate diffusion. We generalize the notion of criticality for PKS and show that subcritical problems are globally well-posed. For a fairly general class of problems, we prove the existence of a critical mass which sharply divides the possibility of finite time blow up and global existence. Moreover, we compute the critical mass for fully general problems and show that solutions with smaller mass exists globally. For a class of supercritical problems we prove finite time blow up is possible for initial data of arbitrary mass.Comment: 31 page

Customizable and scalable automated assessment of C/C++ programming assignments

The correction of exercises in programming courses is a laborious task that has traditionally been performed in a manual way. This situation, in turn, delays the access by students to feedback that can contribute significantly to their training as future professionals. Over the years, several approaches have been proposed to automate the assessment of students' programs. Static analysis is a known technique that can partially simulate the process of manual code review performed by lecturers. As such, it is a plausible option to assess whether students' solutions meet the requirements imposed on the assignments. However, implementing a personalized analysis beyond the rules included in existing tools may be a complex task for the lecturer without a mechanism that guides the work. In this paper, we present a method to provide automated and specific feedback to immediately inform students about their mistakes in programming courses. To that end, we developed the CAC++ library, which enables constructing tailored static analysis programs for C/C++ practices. The library allows for great flexibility and personalization of verifications to adjust them to each particular task, overcoming the limitations of most of the existing assessment tools. Our approach to providing specific feedback has been evaluated for a period of three academic years in a course related to object-oriented programming. The library allowed lecturers to reduce the size of the static analysis programs developed for this course. During this period, the academic results improved and undergraduates positively valued the aid offered when undertaking the implementation of assignments.Universidad de Cádiz, Grant/Award Numbers: sol-201500054192-tra, sol-201600064680-tra; Ministerio de Ciencia, Innovación y Universidades, Grant/Award Number: RTI2018-093608-B-C33; European Regional Development Fun

Particle approximation of the one dimensional Keller-Segel equation, stability and rigidity of the blow-up

We investigate a particle system which is a discrete and deterministic approximation of the one-dimensional Keller-Segel equation with a logarithmic potential. The particle system is derived from the gradient flow of the homogeneous free energy written in Lagrangian coordinates. We focus on the description of the blow-up of the particle system, namely: the number of particles involved in the first aggregate, and the limiting profile of the rescaled system. We exhibit basins of stability for which the number of particles is critical, and we prove a weak rigidity result concerning the rescaled dynamics. This work is complemented with a detailed analysis of the case where only three particles interact